1
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Dong Y, Xu X, Qian L, Kou Z, Andongma AA, Zhou L, Huang Y, Wang Y. Genome-wide identification of yellow gene family in Hermetia illucens and functional analysis of yellow-y by CRISPR/Cas9. INSECT SCIENCE 2024. [PMID: 38685755 DOI: 10.1111/1744-7917.13371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 05/02/2024]
Abstract
The yellow gene family plays a crucial role in insect pigmentation. It has potential for use as a visible marker gene in genetic manipulation and transgenic engineering in several model and non-model insects. Sadly, yellow genes have rarely been identified in Stratiomyidae species and the functions of yellow genes are relatively unknown. In the present study, we first manually annotated and curated 10 yellow genes in the black soldier fly (BSF), Hermetia illucens (Stratiomyidae). Then, the conserved amino acids in the major royal jelly proteins (MRJPs) domain, structural architecture and phylogenetic relationship of yellow genes in BSF were analyzed. We found that the BSF yellow-y, yellow-c and yellow-f genes are expressed at all developmental stages, especially in the prepupal stage. Using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, we successfully disrupted yellow-y, yellow-c and yellow-f in the BSF. Consequently, the mutation of yellow-y clearly resulted in a pale-yellow body color in prepupae, pupae and adults, instead of the typical black body color of the wild type. However, the mutation of yellow-c or yellow-f genes did not result in any change in color of the insects, when compared with the wild type. Our study indicates that the BSF yellow-y gene plays a role in body pigmentation, providing an optimal marker gene for the genetic manipulation of BSF.
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Affiliation(s)
- Yongcheng Dong
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Xiaomiao Xu
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Lansa Qian
- Chinese Academy of Sciences (CAS) Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, CAS, Shanghai, China
| | - Zongqing Kou
- Chinese Academy of Sciences (CAS) Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, CAS, Shanghai, China
| | - Awawing A Andongma
- Insect and Parasite Ecology Group, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Lijun Zhou
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yongping Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yaohui Wang
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
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2
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Zhang J, Cong Q, Shen J, Song L, Hallwachs W, Janzen DH, Sourakov A, Grishin NV. What one genus of showy moths can say about migration, adaptation, and wing pattern. Proc Natl Acad Sci U S A 2024; 121:e2319726121. [PMID: 38630713 PMCID: PMC11047066 DOI: 10.1073/pnas.2319726121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
The Ornate Moth, Utetheisa ornatrix, has served as a model species in chemical ecology studies for decades. Like in the widely publicized stories of the Monarch and other milkweed butterflies, the Ornate Moth and its relatives are tropical insects colonizing whole continents assisted by their chemical defenses. With the recent advances in genomic techniques and evo-devo research, it is becoming a model for studies in other areas, from wing pattern development to phylogeography, from toxicology to epigenetics. We used a genomic approach to learn about Utetheisa's evolution, detoxification, dispersal abilities, and wing pattern diversity. We present an evolutionary genomic analysis of the worldwide genus Utetheisa, then focusing on U. ornatrix. Our reference genome of U. ornatrix reveals gene duplications in the regions possibly associated with detoxification abilities, which allows them to feed on toxic food plants. Finally, comparative genomic analysis of over 100 U. ornatrix specimens from the museum with apparent differences in wing patterns suggest the potential roles of cortex and lim3 genes in wing pattern formation of Lepidoptera and the utility of museum-preserved collection specimens for wing pattern research.
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Affiliation(s)
- Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jinhui Shen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Leina Song
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Daniel H. Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Andrei Sourakov
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL32611
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75390
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3
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Ridgway AM, Hood EJ, Jimenez JF, Nunes MDS, McGregor AP. Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species. Curr Biol 2024; 34:1114-1121.e7. [PMID: 38309269 DOI: 10.1016/j.cub.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/02/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
The emergence and diversification of morphological novelties is a major feature of animal evolution.1,2,3,4,5,6,7,8,9 However, relatively little is known about the genetic basis of the evolution of novel structures and the mechanisms underlying their diversification. The epandrial posterior lobes of male genitalia are a novelty of particular Drosophila species.10,11,12,13 The lobes grasp the female ovipositor and insert between her abdominal tergites and, therefore, are important for copulation and species recognition.10,11,12,14,15,16,17 The posterior lobes likely evolved from co-option of a Hox-regulated gene network from the posterior spiracles10 and have since diversified in morphology in the D. simulans clade, in particular, over the last 240,000 years, driven by sexual selection.18,19,20,21 The genetic basis of this diversification is polygenic but, to the best of our knowledge, none of the causative genes have been identified.22,23,24,25,26,27,28,29,30 Identifying the genes underlying the diversification of these secondary sexual structures is essential to understanding the evolutionary impact on copulation and species recognition. Here, we show that Sox21b negatively regulates posterior lobe size. This is consistent with expanded Sox21b expression in D. mauritiana, which develops smaller posterior lobes than D. simulans. We tested this by generating reciprocal hemizygotes and confirmed that changes in Sox21b underlie posterior lobe evolution between these species. Furthermore, we found that posterior lobe size differences caused by the species-specific allele of Sox21b significantly affect copulation duration. Taken together, our study reveals the genetic basis for the sexual-selection-driven diversification of a novel morphological structure and its functional impact on copulatory behavior.
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Affiliation(s)
- Amber M Ridgway
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Emily J Hood
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | | | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK.
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4
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Wang S, Girardello M, Zhang W. Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics. J Genet Genomics 2024; 51:292-301. [PMID: 37302475 DOI: 10.1016/j.jgg.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
Mountains are rich in biodiversity, and butterflies are species-rich and have a good ecological and evolutionary research foundation. This review addresses the potential and progress of studying mountain biodiversity using butterflies as a model. We discuss the uniqueness of mountain ecosystems, factors influencing the distribution of mountain butterflies, representative genetic and evolutionary models in butterfly research, and evolutionary studies of mountain biodiversity involving butterfly genetics and genomics. Finally, we demonstrate the necessity of studying mountain butterflies and propose future perspectives. This review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.
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Affiliation(s)
- Shuting Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Marco Girardello
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, Faculdade de Ciências Agrárias e do Ambiente, Universidade dos Açores, 9700-042 Angra do Heroísmo, Terceira, Portugal
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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5
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Teng D, Zhang W. The diversification of butterfly wing patterns: progress and prospects. CURRENT OPINION IN INSECT SCIENCE 2024; 61:101137. [PMID: 37922984 DOI: 10.1016/j.cois.2023.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Butterfly wings display rich phenotypic diversity and are associated with complex biological functions, thus serving as an important evolutionary system to address the genetic basis and evolution of phenotypic diversification. We review recent butterfly studies that revealed complex functions underlying diversified wing patterns and describe the genetic and environmental factors involved in wing pattern determinations. These factors lead to inter-specific divergence, genetic polymorphism, and phenotypic plasticity, which in many cases are decided by several key genes. We also summarize the research advances on gene co-option as an important origin of functional complexity and evolutionary novelty. These findings reveal a pattern of evolutionary innovation within a constrained developmental framework during butterfly wing morphogenesis, but further research is required to gain a systematic and comprehensive understanding.
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Affiliation(s)
- Dequn Teng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Medog Biodiversity Observation and Research Station of Tibet Autonomous Region, Nyingchi 860711, China.
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6
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Llaurens V. A colourful duplication. eLife 2023; 12:e92763. [PMID: 37917141 PMCID: PMC10622141 DOI: 10.7554/elife.92763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A genetic duplication event during evolution allowed male wood tiger moths to have either yellow or white patterns on their wings.
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Affiliation(s)
- Violaine Llaurens
- Centre national de la recherche scientifique (CNRS)ParisFrance
- Muséum national d'Histoire naturelleParisFrance
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7
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Thayer RC, Patel NH. A meta-analysis of butterfly structural colors: their color range, distribution and biological production. J Exp Biol 2023; 226:jeb245940. [PMID: 37937662 DOI: 10.1242/jeb.245940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Butterfly scales are among the richest natural sources of optical nanostructures, which produce structural color and iridescence. Several recurring nanostructure types have been described, such as ridge multilayers, gyroids and lower lamina thin films. While the optical mechanisms of these nanostructure classes are known, their phylogenetic distributions and functional ranges have not been described in detail. In this Review, we examine a century of research on the biological production of structural colors, including their evolution, development and genetic regulation. We have also created a database of more than 300 optical nanostructures in butterflies and conducted a meta-analysis of the color range, abundance and phylogenetic distribution of each nanostructure class. Butterfly structural colors are ubiquitous in short wavelengths but extremely rare in long wavelengths, especially red. In particular, blue wavelengths (around 450 nm) occur in more clades and are produced by more kinds of nanostructures than other hues. Nanostructure categories differ in prevalence, phylogenetic distribution, color range and brightness. For example, lamina thin films are the least bright; perforated lumen multilayers occur most often but are almost entirely restricted to the family Lycaenidae; and 3D photonic crystals, including gyroids, have the narrowest wavelength range (from about 450 to 550 nm). We discuss the implications of these patterns in terms of nanostructure evolution, physical constraint and relationships to pigmentary color. Finally, we highlight opportunities for future research, such as analyses of subadult and Hesperid structural colors and the identification of genes that directly build the nanostructures, with relevance for biomimetic engineering.
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Affiliation(s)
- Rachel C Thayer
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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8
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Brien MN, Orteu A, Yen EC, Galarza JA, Kirvesoja J, Pakkanen H, Wakamatsu K, Jiggins CD, Mappes J. Colour polymorphism associated with a gene duplication in male wood tiger moths. eLife 2023; 12:e80116. [PMID: 37902626 PMCID: PMC10635649 DOI: 10.7554/elife.80116] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/05/2023] [Indexed: 10/31/2023] Open
Abstract
Colour is often used as an aposematic warning signal, with predator learning expected to lead to a single colour pattern within a population. However, there are many puzzling cases where aposematic signals are also polymorphic. The wood tiger moth, Arctia plantaginis, displays bright hindwing colours associated with unpalatability, and males have discrete colour morphs which vary in frequency between localities. In Finland, both white and yellow morphs can be found, and these colour morphs also differ in behavioural and life-history traits. Here, we show that male colour is linked to an extra copy of a yellow family gene that is only present in the white morphs. This white-specific duplication, which we name valkea, is highly upregulated during wing development. CRISPR targeting valkea resulted in editing of both valkea and its paralog, yellow-e, and led to the production of yellow wings. We also characterise the pigments responsible for yellow, white, and black colouration, showing that yellow is partly produced by pheomelanins, while black is dopamine-derived eumelanin. Our results add to a growing number of studies on the genetic architecture of complex and seemingly paradoxical polymorphisms, and the role of gene duplications and structural variation in adaptive evolution.
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Affiliation(s)
- Melanie N Brien
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of HelsinkiHelsinkiFinland
| | - Anna Orteu
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Eugenie C Yen
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Juan A Galarza
- Ecology and Genetics Research Unit, University of OuluOuluFinland
| | - Jimi Kirvesoja
- Department of Biological and Environmental Science, University of JyväskyläJyväskyläFinland
| | - Hannu Pakkanen
- Department of Chemistry, University of JyväskyläJyväskyläFinland
| | | | - Chris D Jiggins
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Johanna Mappes
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of HelsinkiHelsinkiFinland
- Department of Biological and Environmental Science, University of JyväskyläJyväskyläFinland
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9
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Seah KS, Saranathan V. Hierarchical morphogenesis of swallowtail butterfly wing scale nanostructures. eLife 2023; 12:RP89082. [PMID: 37768710 PMCID: PMC10538957 DOI: 10.7554/elife.89082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
The study of color patterns in the animal integument is a fundamental question in biology, with many lepidopteran species being exemplary models in this endeavor due to their relative simplicity and elegance. While significant advances have been made in unraveling the cellular and molecular basis of lepidopteran pigmentary coloration, the morphogenesis of wing scale nanostructures involved in structural color production is not well understood. Contemporary research on this topic largely focuses on a few nymphalid model taxa (e.g., Bicyclus, Heliconius), despite an overwhelming diversity in the hierarchical nanostructural organization of lepidopteran wing scales. Here, we present a time-resolved, comparative developmental study of hierarchical scale nanostructures in Parides eurimedes and five other papilionid species. Our results uphold the putative conserved role of F-actin bundles in acting as spacers between developing ridges, as previously documented in several nymphalid species. Interestingly, while ridges are developing in P. eurimedes, plasma membrane manifests irregular mesh-like crossribs characteristic of Papilionidae, which delineate the accretion of cuticle into rows of planar disks in between ridges. Once the ridges have grown, disintegrating F-actin bundles appear to reorganize into a network that supports the invagination of plasma membrane underlying the disks, subsequently forming an extruded honeycomb lattice. Our results uncover a previously undocumented role for F-actin in the morphogenesis of complex wing scale nanostructures, likely specific to Papilionidae.
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Affiliation(s)
- Kwi Shan Seah
- Division of Science, Yale-NUS CollegeSingaporeSingapore
- Department of Biological Science, National University of SingaporeSingaporeSingapore
| | - Vinodkumar Saranathan
- Division of Science, Yale-NUS CollegeSingaporeSingapore
- Department of Biological Science, National University of SingaporeSingaporeSingapore
- NUS Nanoscience and Nanotechnology Initiative (NUSNNI-NanoCore), National University of SingaporeSingaporeSingapore
- Lee Kong Chian Natural History Museum, National University of SingaporeSingaporeSingapore
- Present Address: Division of Sciences, School of Interwoven Arts and Sciences, Krea University, Central ExpresswaySri CityIndia
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Hanly JJ, Loh LS, Mazo-Vargas A, Rivera-Miranda TS, Livraghi L, Tendolkar A, Day CR, Liutikaite N, Earls EA, Corning OBWH, D'Souza N, Hermina-Perez JJ, Mehta C, Ainsworth JA, Rossi M, Papa R, McMillan WO, Perry MW, Martin A. Frizzled2 receives WntA signaling during butterfly wing pattern formation. Development 2023; 150:dev201868. [PMID: 37602496 PMCID: PMC10560568 DOI: 10.1242/dev.201868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Butterfly color patterns provide visible and biodiverse phenotypic readouts of the patterning processes. Although the secreted ligand WntA has been shown to instruct the color pattern formation in butterflies, its mode of reception remains elusive. Butterfly genomes encode four homologs of the Frizzled-family of Wnt receptors. Here, we show that CRISPR mosaic knockouts of frizzled2 (fz2) phenocopy the color pattern effects of WntA loss of function in multiple nymphalids. Whereas WntA mosaic clones result in intermediate patterns of reduced size, fz2 clones are cell-autonomous, consistent with a morphogen function. Shifts in expression of WntA and fz2 in WntA crispant pupae show that they are under positive and negative feedback, respectively. Fz1 is required for Wnt-independent planar cell polarity in the wing epithelium. Fz3 and Fz4 show phenotypes consistent with Wnt competitive-antagonist functions in vein formation (Fz3 and Fz4), wing margin specification (Fz3), and color patterning in the Discalis and Marginal Band Systems (Fz4). Overall, these data show that the WntA/Frizzled2 morphogen-receptor pair forms a signaling axis that instructs butterfly color patterning and shed light on the functional diversity of insect Frizzled receptors.
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Affiliation(s)
- Joseph J. Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Gamboa 0843-03092, Panama
| | - Ling S. Loh
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Anyi Mazo-Vargas
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | | | - Luca Livraghi
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Gamboa 0843-03092, Panama
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Amruta Tendolkar
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Christopher R. Day
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27708, USA
| | - Neringa Liutikaite
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Emily A. Earls
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Olaf B. W. H. Corning
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Natalie D'Souza
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - José J. Hermina-Perez
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Caroline Mehta
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Julia A. Ainsworth
- Department of Cell and Developmental Biology, UC San Diego, La Jolla, CA, USA
| | - Matteo Rossi
- Division of Evolutionary Biology, Ludwig Maximilian University, Munich 80539, Germany
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico at Río Piedras, San Juan 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00931, Puerto Rico
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale, Università di Parma, Parma 43121, Italy
| | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa 0843-03092, Panama
| | - Michael W. Perry
- Department of Cell and Developmental Biology, UC San Diego, La Jolla, CA, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Gamboa 0843-03092, Panama
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11
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Hundsdoerfer AK, Schell T, Patzold F, Wright CJ, Yoshido A, Marec F, Daneck H, Winkler S, Greve C, Podsiadlowski L, Hiller M, Pippel M. High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae). BMC Genomics 2023; 24:443. [PMID: 37550607 PMCID: PMC10405479 DOI: 10.1186/s12864-023-09506-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics. RESULTS The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function. CONCLUSIONS Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).
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Affiliation(s)
- Anna K Hundsdoerfer
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany.
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Franziska Patzold
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | | | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Hana Daneck
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Michael Hiller
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, 751 23, Sweden
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12
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How SHC, Banerjee TD, Monteiro A. Vermilion and cinnabar are involved in ommochrome pigment biosynthesis in eyes but not wings of Bicyclus anynana butterflies. Sci Rep 2023; 13:9368. [PMID: 37296302 PMCID: PMC10256707 DOI: 10.1038/s41598-023-36491-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
If the same pigment is found in different tissues in a body, it is natural to assume that the same metabolic pathways are deployed similarly in each tissue. Here we show that this is not the case for ommochromes, the red and orange pigments found in the eyes and wings of butterflies. We tested the expression and function of vermilion and cinnabar, two known fly genes in the ommochrome pathway, in the development of pigments in the eyes and in the wings of Bicyclus anynana butterflies, both traits having reddish/orange pigments. By using fluorescent in-situ hybridization (HCR3.0) we localized the expression of vermilion and cinnabar in the cytoplasm of pigment cells in the ommatidia but observed no clear expression for either gene on larval and pupal wings. We then disrupted the function of both genes, using CRISPR-Cas9, which resulted in the loss of pigment in the eyes but not in the wings. Using thin-layer chromatography and UV-vis spectroscopy we identified the presence of ommochrome and ommochrome precursors in the orange wing scales and in the hemolymph of pupae. We conclude that the wings either synthesize ommochromes locally, with yet unidentified enzymes or incorporate these pigments synthesized elsewhere from the hemolymph. Different metabolic pathways or transport mechanisms, thus, lead to the presence of ommochromes in the wings and eyes of B. anynana butterflies.
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Affiliation(s)
- Shaun Hong Chuen How
- Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Tirtha Das Banerjee
- Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore.
| | - Antόnia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore.
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13
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Bayala EX, VanKuren N, Massardo D, Kronforst MR. aristaless1 has a dual role in appendage formation and wing color specification during butterfly development. BMC Biol 2023; 21:100. [PMID: 37143075 PMCID: PMC10161628 DOI: 10.1186/s12915-023-01601-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/13/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Highly diverse butterfly wing patterns have emerged as a powerful system for understanding the genetic basis of phenotypic variation. While the genetic basis of this pattern variation is being clarified, the precise developmental pathways linking genotype to phenotype are not well understood. The gene aristaless, which plays a role in appendage patterning and extension, has been duplicated in Lepidoptera. One copy, aristaless1, has been shown to control a white/yellow color switch in the butterfly Heliconius cydno, suggesting a novel function associated with color patterning and pigmentation. Here we investigate the developmental basis of al1 in embryos, larvae, and pupae using new antibodies, CRISPR/Cas9, RNAi, qPCR assays of downstream targets, and pharmacological manipulation of an upstream activator. RESULTS We find that Al1 is expressed at the distal tips of developing embryonic appendages consistent with its ancestral role. In developing wings, we observe Al1 accumulation within developing scale cells of white H. cydno during early pupation while yellow scale cells exhibit little Al1 at this time point. Reduced Al1 expression is also associated with yellow scale development in al1 knockouts and knockdowns. We propose that Al1 expression in future white scales might be related to an observed downregulation of the enzyme Cinnabar and other genes that synthesize and transport the yellow pigment, 3-hydroxykynurenine (3-OHK). Finally, we provide evidence that Al1 activation is under the control of Wnt signaling. CONCLUSIONS We propose a model in which high levels of Al1 during early pupation, which are mediated by Wnt, are important for melanic pigmentation and specifying white portions of the wing while reduced levels of Al1 during early pupation promote upregulation of proteins needed to move and synthesize 3-OHK, promoting yellow pigmentation. In addition, we discuss how the ancestral role of aristaless in appendage extension may be relevant in understanding the cellular mechanism behind color patterning in the context of the heterochrony hypothesis.
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Affiliation(s)
- Erick X Bayala
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, 60637, USA.
| | - Nicholas VanKuren
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Darli Massardo
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, 60637, USA
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14
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Wee JLQ, Murugesan SN, Wheat CW, Monteiro A. The genetic basis of wing spots in Pieris canidia butterflies. BMC Genomics 2023; 24:169. [PMID: 37016295 PMCID: PMC10074818 DOI: 10.1186/s12864-023-09261-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
Spots in pierid butterflies and eyespots in nymphalid butterflies are likely non-homologous wing colour pattern elements, yet they share a few features in common. Both develop black scales that depend on the function of the gene spalt, and both might have central signalling cells. This suggests that both pattern elements may be sharing common genetic circuitry. Hundreds of genes have already been associated with the development of nymphalid butterfly eyespot patterns, but the genetic basis of the simpler spot patterns on the wings of pierid butterflies has not been investigated. To facilitate studies of pierid wing patterns, we report a high-quality draft genome assembly for Pieris canidia, the Indian cabbage white. We then conducted transcriptomic analyses of pupal wing tissues sampled from the spot and non-spot regions of P. canidia at 3-6 h post-pupation. A total of 1352 genes were differentially regulated between wing tissues with and without the black spot, including spalt, Krüppel-like factor 10, genes from the Toll, Notch, TGF-β, and FGFR signalling pathways, and several genes involved in the melanin biosynthetic pathway. We identified 14 genes that are up-regulated in both pierid spots and nymphalid eyespots and propose that spots and eyespots share regulatory modules despite their likely independent origins.
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Affiliation(s)
- Jocelyn Liang Qi Wee
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
| | - Suriya Narayanan Murugesan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
| | | | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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15
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Pan Z, Ding Y, Zhang S, Li L, Ma F. Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae). INSECTS 2023; 14:304. [PMID: 36975989 PMCID: PMC10058580 DOI: 10.3390/insects14030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.
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Affiliation(s)
- Zhixiang Pan
- School of Life Sciences, Taizhou University, Taizhou 318000, China
| | - Yinhuan Ding
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China
| | - Shusheng Zhang
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou 325500, China
| | - Luxian Li
- Zhejiang Environment Technology Company Limited, Hangzhou 311100, China
| | - Fangzhou Ma
- Nanjing Institute of Environmental Sciences under Ministry of Ecology and Environment, Nanjing 210042, China
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16
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Van Belleghem SM, Ruggieri AA, Concha C, Livraghi L, Hebberecht L, Rivera ES, Ogilvie JG, Hanly JJ, Warren IA, Planas S, Ortiz-Ruiz Y, Reed R, Lewis JJ, Jiggins CD, Counterman BA, McMillan WO, Papa R. High level of novelty under the hood of convergent evolution. Science 2023; 379:1043-1049. [PMID: 36893249 PMCID: PMC11000492 DOI: 10.1126/science.ade0004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/08/2023] [Indexed: 03/11/2023]
Abstract
Little is known about the extent to which species use homologous regulatory architectures to achieve phenotypic convergence. By characterizing chromatin accessibility and gene expression in developing wing tissues, we compared the regulatory architecture of convergence between a pair of mimetic butterfly species. Although a handful of color pattern genes are known to be involved in their convergence, our data suggest that different mutational paths underlie the integration of these genes into wing pattern development. This is supported by a large fraction of accessible chromatin being exclusive to each species, including the de novo lineage-specific evolution of a modular optix enhancer. These findings may be explained by a high level of developmental drift and evolutionary contingency that occurs during the independent evolution of mimicry.
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Affiliation(s)
- Steven M. Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, Leuven, Belgium
| | - Angelo A. Ruggieri
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Carolina Concha
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Luca Livraghi
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Laura Hebberecht
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- School of Biological Sciences, Bristol University, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Edgardo Santiago Rivera
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biomaterials, Universität Bayreuth, Bayreuth, Germany
| | - James G. Ogilvie
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Joseph J. Hanly
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Silvia Planas
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Yadira Ortiz-Ruiz
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Robert Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - James J. Lewis
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | | | | | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
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17
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Feigin C, Li S, Moreno J, Mallarino R. The GRN concept as a guide for evolutionary developmental biology. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:92-104. [PMID: 35344632 PMCID: PMC9515236 DOI: 10.1002/jez.b.23132] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022]
Abstract
Organismal phenotypes result largely from inherited developmental programs, usually executed during embryonic and juvenile life stages. These programs are not blank slates onto which natural selection can draw arbitrary forms. Rather, the mechanisms of development play an integral role in shaping phenotypic diversity and help determine the evolutionary trajectories of species. Modern evolutionary biology must, therefore, account for these mechanisms in both theory and in practice. The gene regulatory network (GRN) concept represents a potent tool for achieving this goal whose utility has grown in tandem with advances in "omic" technologies and experimental techniques. However, while the GRN concept is widely utilized, it is often less clear what practical implications it has for conducting research in evolutionary developmental biology. In this Perspective, we attempt to provide clarity by discussing how experiments and projects can be designed in light of the GRN concept. We first map familiar biological notions onto the more abstract components of GRN models. We then review how diverse functional genomic approaches can be directed toward the goal of constructing such models and discuss current methods for functionally testing evolutionary hypotheses that arise from them. Finally, we show how the major steps of GRN model construction and experimental validation suggest generalizable workflows that can serve as a scaffold for project design. Taken together, the practical implications that we draw from the GRN concept provide a set of guideposts for studies aiming at unraveling the molecular basis of phenotypic diversity.
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Affiliation(s)
- Charles Feigin
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA,School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Jorge Moreno
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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18
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Single-cell atavism reveals an ancient mechanism of cell type diversification in a sea anemone. Nat Commun 2023; 14:885. [PMID: 36797294 PMCID: PMC9935875 DOI: 10.1038/s41467-023-36615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Cnidocytes are the explosive stinging cells unique to cnidarians (corals, jellyfish, etc). Specialized for prey capture and defense, cnidocytes comprise a group of over 30 morphologically and functionally distinct cell types. These unusual cells are iconic examples of biological novelty but the developmental mechanisms driving diversity of the stinging apparatus are poorly characterized, making it challenging to understand the evolutionary history of stinging cells. Using CRISPR/Cas9-mediated genome editing in the sea anemone Nematostella vectensis, we show that a single transcription factor (NvSox2) acts as a binary switch between two alternative stinging cell fates. Knockout of NvSox2 causes a transformation of piercing cells into ensnaring cells, which are common in other species of sea anemone but appear to have been silenced in N. vectensis. These results reveal an unusual case of single-cell atavism and expand our understanding of the diversification of cell type identity.
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19
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The Genetic Mechanisms Underlying the Concerted Expression of the yellow and tan Genes in Complex Patterns on the Abdomen and Wings of Drosophila guttifera. Genes (Basel) 2023; 14:genes14020304. [PMID: 36833231 PMCID: PMC9957387 DOI: 10.3390/genes14020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here, we sought to identify the genetic mechanisms that regulate the tan (t) gene in a multi-spotted pigmentation pattern on the abdomen and wings of Drosophila guttifera. Previously, we showed that yellow (y) gene expression completely prefigures the abdominal and wing pigment patterns of this species. In the current study, we demonstrate that the t gene is co-expressed with the y gene in nearly identical patterns, both transcripts foreshadowing the adult abdominal and wing melanin spot patterns. We identified cis-regulatory modules (CRMs) of t, one of which drives reporter expression in six longitudinal rows of spots on the developing pupal abdomen, while the second CRM activates the reporter gene in a spotted wing pattern. Comparing the abdominal spot CRMs of y and t, we found a similar composition of putative transcription factor binding sites that are thought to regulate the complex expression patterns of both terminal pigmentation genes y and t. In contrast, the y and t wing spots appear to be regulated by distinct upstream factors. Our results suggest that the D. guttifera abdominal and wing melanin spot patterns have been established through the co-regulation of y and t, shedding light on how complex morphological traits may be regulated through the parallel coordination of downstream target genes.
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20
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Lactobacillus for ribosome peptide editing cancer. Clin Transl Oncol 2023; 25:1522-1544. [PMID: 36694080 PMCID: PMC9873400 DOI: 10.1007/s12094-022-03066-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/24/2022] [Indexed: 01/25/2023]
Abstract
This study reviews newly discovered insect peptide point mutations as new possible cancer research targets. To interpret newly discovered peptide point mutations in insects as new possible cancer research targets, we focused on the numerous peptide changes found in the 'CSP' family on the sex pheromone gland of the female silkworm moth Bombyx mori. We predict that the Bombyx peptide modifications will have a significant effect on cancer CUP (cancers of unknown primary) therapy and that bacterial peptide editing techniques, specifically Lactobacillus combined to CRISPR, will be used to regulate ribosomes and treat cancer in humans.
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21
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Functional genomic tools for emerging model species. Trends Ecol Evol 2022; 37:1104-1115. [PMID: 35914975 DOI: 10.1016/j.tree.2022.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/12/2023]
Abstract
Most studies in the field of ecology and evolution aiming to connect genotype to phenotype rarely validate identified loci using functional tools. Recent developments in RNA interference (RNAi) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas genome editing have dramatically increased the feasibility of functional validation. However, these methods come with specific challenges when applied to emerging model organisms, including limited spatial control of gene silencing, low knock-in efficiencies, and low throughput of functional validation. Moreover, many functional studies to date do not recapitulate ecologically relevant variation, and this limits their scope for deeper insights into evolutionary processes. We therefore argue that increased use of gene editing by allelic replacement through homology-directed repair (HDR) would greatly benefit the field of ecology and evolution.
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22
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Chan WP, Rabideau Childers R, Ashe S, Tsai CC, Elson C, Keleher KJ, Sipe RLH, Maier CA, Sourakov A, Gall LF, Bernard GD, Soucy ER, Yu N, Pierce NE. A high-throughput multispectral imaging system for museum specimens. Commun Biol 2022; 5:1318. [PMID: 36456867 PMCID: PMC9715708 DOI: 10.1038/s42003-022-04282-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
We present an economical imaging system with integrated hardware and software to capture multispectral images of Lepidoptera with high efficiency. This method facilitates the comparison of colors and shapes among species at fine and broad taxonomic scales and may be adapted for other insect orders with greater three-dimensionality. Our system can image both the dorsal and ventral sides of pinned specimens. Together with our processing pipeline, the descriptive data can be used to systematically investigate multispectral colors and shapes based on full-wing reconstruction and a universally applicable ground plan that objectively quantifies wing patterns for species with different wing shapes (including tails) and venation systems. Basic morphological measurements, such as body length, thorax width, and antenna size are automatically generated. This system can increase exponentially the amount and quality of trait data extracted from museum specimens.
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Affiliation(s)
- Wei-Ping Chan
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Richard Rabideau Childers
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Sorcha Ashe
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Cheng-Chia Tsai
- grid.21729.3f0000000419368729Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY USA
| | - Caroline Elson
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kirsten J. Keleher
- grid.40803.3f0000 0001 2173 6074Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC USA ,grid.5386.8000000041936877XDepartment of Neurobiology and Behavior, Cornell University, Ithaca, NY USA
| | - Rachel L. Hawkins Sipe
- grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Crystal A. Maier
- grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Andrei Sourakov
- grid.15276.370000 0004 1936 8091McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL USA
| | - Lawrence F. Gall
- grid.47100.320000000419368710Computer Systems Office & Division of Entomology, Peabody Museum of Natural History, Yale University, New Haven, CT USA
| | - Gary D. Bernard
- grid.34477.330000000122986657Department of Electrical and Computer Engineering, University of Washington, Seattle, WA USA
| | - Edward R. Soucy
- grid.38142.3c000000041936754XCenter for Brain Science, Harvard University, Cambridge, MA USA
| | - Nanfang Yu
- grid.21729.3f0000000419368729Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY USA
| | - Naomi E. Pierce
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
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23
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Otaki JM, Nakazato Y. Butterfly Wing Color Pattern Modification Inducers May Act on Chitin in the Apical Extracellular Site: Implications in Morphogenic Signals for Color Pattern Determination. BIOLOGY 2022; 11:1620. [PMID: 36358322 PMCID: PMC9687432 DOI: 10.3390/biology11111620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 09/28/2023]
Abstract
Butterfly wing color patterns are modified by various treatments, such as temperature shock, injection of chemical inducers, and covering materials on pupal wing tissue. Their mechanisms of action have been enigmatic. Here, we investigated the mechanisms of color pattern modifications usingthe blue pansy butterfly Junoniaorithya. We hypothesized that these modification-inducing treatments act on the pupal cuticle or extracellular matrix (ECM). Mechanical load tests revealed that pupae treated with cold shock or chemical inducers were significantly less rigid, suggesting that these treatments made cuticle formation less efficient. A known chitin inhibitor, FB28 (fluorescent brightener 28), was discovered to efficiently induce modifications. Taking advantage of its fluorescent character, fluorescent signals from FB28 were observed in live pupae in vivo from the apical extracellular side and were concentrated at the pupal cuticle focal spots immediately above the eyespot organizing centers. It was shown that chemical modification inducers and covering materials worked additively. Taken together, various modification-inducing treatments likely act extracellularly on chitin or other polysaccharides to inhibit pupal cuticle formation or ECM function, which probably causes retardation of morphogenic signals. It is likely that an interactive ECM is required for morphogenic signals for color pattern determination to travel long distances.
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Affiliation(s)
- Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa 903-0213, Japan
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24
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Thulluru A, Saad L, Nagah Abdou Y, Martin A, Kee HL. CRISPR in butterflies: An undergraduate lab experience to inactivate wing patterning genes during development. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:605-619. [PMID: 36054482 DOI: 10.1002/bmb.21669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 06/13/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
CRISPR is a technique increasingly used in the laboratory for both fundamental and applied research. We designed and implemented a lab experience for undergraduates to carry out CRISPR technology in the lab, and knockout the wing patterning genes optix and WntA in Vanessa cardui butterflies. Students obtained spectacular phenotypic mutants of butterfly wings color and patterns, awakening curiosity about how genomes encode morphology. In addition, students successfully used molecular techniques to genotype and screen wild-type caterpillar larvae and butterflies for CRISPR edits in genes. Student feedback suggests that they experienced a meaningful process of scientific inquiry by carrying out the whole CRISPR workflow process, from the design and delivery of CRISPR components through microinjection of butterfly eggs, the rearing of live animals through their complete life cycle, and molecular and phenotypic analyses of the resulting mutants. We discuss our experience using CRISP genome editing experiments in butterflies to expose students to hands-on research experiences probing gene-to-phenotype relationships in a charismatic and live organism.
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Affiliation(s)
- Aamani Thulluru
- Department of Biology, Stetson University, DeLand, Florida, USA
| | - Luisa Saad
- Department of Biology, Stetson University, DeLand, Florida, USA
| | | | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Hooi Lynn Kee
- Department of Biology, Stetson University, DeLand, Florida, USA
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25
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Espeland M, Podsiadlowski L. How butterfly wings got their pattern. Science 2022; 378:249-250. [PMID: 36264812 DOI: 10.1126/science.ade5689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Gene regulatory elements play a crucial role in the pattern formation of butterfly wings.
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Affiliation(s)
- Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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26
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Kumagai H, Kondo K, Kunieda T. Application of CRISPR/Cas9 system and the preferred no-indel end-joining repair in tardigrades. Biochem Biophys Res Commun 2022; 623:196-201. [PMID: 35926276 DOI: 10.1016/j.bbrc.2022.07.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 12/20/2022]
Abstract
Tardigrades are small aquatic animals known for the tolerant ability against various extreme stresses. Recent studies identified several tardigrade-unique proteins as protective factors of biomolecules from extreme stresses. Due to the limitation of the technique available in tardigrades, the function of these protective molecules has largely been studied utilizing the systems of in vitro and the heterologous expression in other organisms. Although RNAi is feasible in tardigrades, their effects are variable and not always sufficient. To analyze the functions of the tardigrade protective proteins, in vivo genetic manipulations have been desired. In this study, we used a tardigrade Hypsibius exemplaris as a model whose genome is available, and developed the delivery method of Cas9 ribonucleoproteins (RNPs) to adult tardigrade cells. Cas9 RNPs containing two kinds of crRNAs were injected to the body cavity of adult tardigrades and subjected to the subsequent electroporation to facilitate the incorporation of RNPs to the cells. Using this delivery method, we detected the deletion of the intervening region between two crRNAs from the genome. Intriguingly, all examined joining sites exhibited no incorporation of insertions/deletions (indels), suggesting that no-indel end-joining is dominant repair system in this tardigrade. We also detected similar removal of the intervening region even in the tardigrades injected with Cas9 RNPs without electroporation and in this case the no-indel end-joining is detected in still dominant but not all examined joining sites. This study provides the development of the delivery method of Cas9 RNPs to tardigrade cells and our data also suggested that simultaneous application of more than two crRNAs/gRNAs are recommended to disrupt the target gene by CRISPR/Cas9 system to avoid scarless repair in the tardigrade.
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Affiliation(s)
- Hitomi Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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27
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Additive genetic effects in interacting species jointly determine the outcome of caterpillar herbivory. Proc Natl Acad Sci U S A 2022; 119:e2206052119. [PMID: 36037349 PMCID: PMC9456756 DOI: 10.1073/pnas.2206052119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant-insect interactions are common and important in basic and applied biology. Trait and genetic variation can affect the outcome and evolution of these interactions, but the relative contributions of plant and insect genetic variation and how these interact remain unclear and are rarely subject to assessment in the same experimental context. Here, we address this knowledge gap using a recent host-range expansion onto alfalfa by the Melissa blue butterfly. Common garden rearing experiments and genomic data show that caterpillar performance depends on plant and insect genetic variation, with insect genetics contributing to performance earlier in development and plant genetics later. Our models of performance based on caterpillar genetics retained predictive power when applied to a second common garden. Much of the plant genetic effect could be explained by heritable variation in plant phytochemicals, especially saponins, peptides, and phosphatidyl cholines, providing a possible mechanistic understanding of variation in the species interaction. We find evidence of polygenic, mostly additive effects within and between species, with consistent effects of plant genotype on growth and development across multiple butterfly species. Our results inform theories of plant-insect coevolution and the evolution of diet breadth in herbivorous insects and other host-specific parasites.
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28
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Wu MM, Chen X, Xu QX, Zang LS, Wang S, Li M, Xiao D. Melanin Synthesis Pathway Interruption: CRISPR/Cas9-mediated Knockout of dopa decarboxylase (DDC) in Harmonia axyridis (Coleoptera: Coccinellidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:6694719. [PMID: 36082675 PMCID: PMC9459435 DOI: 10.1093/jisesa/ieac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 05/28/2023]
Abstract
CRISPR/Cas9 technology is a very powerful genome editing tool and has been used in many insect species for functional genomics studies through targeted gene mutagenesis. Here, we successfully established CRISPR/Cas9 research platform in Asian multi-colored ladybird beetle, Harmonia axyridis, an important natural enemy in biological control. In this study, one pivotal gene dopa decarboxylase (DDC) in melanin synthesis was targeted by CRISPR/Cas9 to generate mutants in H. axyridis by CRISPR/Cas9 technology. Our results showed that injection of single guide RNA of the DDC and Cas9 protein into preblastoderm eggs induced one insertion and four deletion (indels) mutant H. axyridis. Mutations of HaDDC gene generated 25% mutant rate with melanin missing phenotype in larva, pupa,l and adult stage. The predation ability of the fourth instar larvae has no significant difference between wild (control) and mutant H. axyridis (G0), while these mutant fourth instar larvae had longer developmental period than that of the wild type. Consequently, the total predation of the fourth instar larvae was significantly increased in H. axyridis mutants comparing with the wild type. These results indicated that the success of CRISPR/Cas9 gene editing in H. axyridis. The gene editing platform in H. axyridis would facilitate the gene function research and promote special strain of predatory ladybird beetle generation.
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Affiliation(s)
| | | | - Qing-xuan Xu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lian-sheng Zang
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering of Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Su Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ming Li
- Corresponding author, e-mail: (M.L.), (D.X.)
| | - Da Xiao
- Corresponding author, e-mail: (M.L.), (D.X.)
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29
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Ansai S, Kitano J. Speciation and adaptation research meets genome editing. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200516. [PMID: 35634923 PMCID: PMC9149800 DOI: 10.1098/rstb.2020.0516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/07/2022] [Indexed: 07/20/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations. We describe examples of their application to demonstrate functional analysis of naturally occurring genetic variations and discuss how these technologies can be applied to speciation and adaptation research. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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30
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Komata S, Lin CP, Fujiwara H. doublesex Controls Both Hindwing and Abdominal Mimicry Traits in the Female-Limited Batesian Mimicry of Papilio memnon. FRONTIERS IN INSECT SCIENCE 2022; 2:929518. [PMID: 38468762 PMCID: PMC10926503 DOI: 10.3389/finsc.2022.929518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/20/2022] [Indexed: 03/13/2024]
Abstract
Papilio butterflies are known to possess female-limited Batesian mimicry polymorphisms. In Papilio memnon, females have mimetic and non-mimetic forms, whereas males are monomorphic and non-mimetic. Mimetic females are characterized by color patterns and tails in the hindwing and yellow abdomens. Recently, an analysis of whole-genome sequences has shown that an approximately 160 kb region of chromosome 25 is responsible for mimicry and has high diversity between mimetic (A) and non-mimetic (a) alleles (highly diversified region: HDR). The HDR includes three genes, UXT, doublesex (dsx), and Nach-like, but the functions of these genes are unknown. Here, we investigated the function of dsx, a gene involved in sexual differentiation, which is expected to be functionally important for hindwing and abdominal mimetic traits in P. memnon. Expression analysis by reverse transcription quantitative PCR (RT-qPCR) and RNA sequencing showed that mimetic dsx (dsx-A) was highly expressed in the hindwings in the early pupal stage. In the abdomen, both dsx-A and dsx-a were highly expressed during the early pupal stage. When dsx was knocked down using small interfering RNAs (siRNAs) designed in the common region of dsx-A and dsx-a, a male-like pattern appeared on the hindwings of mimetic and non-mimetic females. Similarly, when dsx was knocked down in the abdomen, the yellow scales characteristic of mimetic females changed to black. Furthermore, when dsx-a was specifically knocked down, the color pattern of the hindwings changed, as in the case of dsx knockdown in non-mimetic females but not mimetic females. These results suggest that dsx-a is involved in color pattern formation on the hindwings of non-mimetic females, whereas dsx-A is involved in hindwing and abdominal mimetic traits. dsx was involved in abdominal and hindwing mimetic traits, but dsx expression patterns in the hindwing and abdomen were different, suggesting that different regulatory mechanisms may exist. Our study is the first to show that the same gene (dsx) regulates both the hindwing and abdominal mimetic traits. This is the first functional analysis of abdominal mimicry in butterflies.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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31
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Antennapedia and optix regulate metallic silver wing scale development and cell shape in Bicyclus anynana butterflies. Cell Rep 2022; 40:111052. [PMID: 35793633 DOI: 10.1016/j.celrep.2022.111052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/06/2022] [Accepted: 06/14/2022] [Indexed: 12/29/2022] Open
Abstract
Butterfly wing scales can develop intricate cuticular nanostructures that produce silver colors, but the underlying genetic and physical basis of such colors is mostly unexplored. Here, we characterize different types of wild-type silver scales in Bicyclus anynana butterflies and show that the varying thickness of the air layer between two cuticular laminas is most important for producing silvery broadband reflectance. We then address the function of five genes-apterous A, Ultrabithorax, doublesex, Antennapedia, and optix-in silver scale development by examining crispants with either ectopic gains or losses of silver scales. Simultaneous transformations of three parameters-loss of the upper lamina, increased lower lamina thickness, and increased pigmentation-occur when silver scales become brown and vice versa when brown scales become silver. Antennapedia and optix are high-level regulators of different silver scale types and determine cell shape in both sexes. Moreover, Antennapedia is involved in determining ridge and crossrib orientation.
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32
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Wee JLQ, Das Banerjee T, Prakash A, Seah KS, Monteiro A. Distal-less and spalt are distal organisers of pierid wing patterns. EvoDevo 2022; 13:12. [PMID: 35659745 PMCID: PMC9164424 DOI: 10.1186/s13227-022-00197-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/06/2022] [Indexed: 11/15/2022] Open
Abstract
Two genes, Distal-less (Dll) and spalt (sal), are known to be involved in establishing nymphalid butterfly wing patterns. They function in several ways: in the differentiation of the eyespot’s central signalling cells, or foci; in the differentiation of the surrounding black disc; in overall scale melanisation (Dll); and in elaborating marginal patterns, such as parafocal elements. However, little is known about the functions of these genes in the development of wing patterns in other butterfly families. Here, we study the expression and function of Dll and sal in the development of spots and other melanic wing patterns of the Indian cabbage white, Pieris canidia, a pierid butterfly. In P. canidia, both Dll and Sal proteins are expressed in the scale-building cells at the wing tips, in chevron patterns along the pupal wing margins, and in areas of future scale melanisation. Additionally, Sal alone is expressed in the future black spots. CRISPR knockouts of Dll and sal showed that each gene is required for the development of melanic wing pattern elements, and repressing pteridine granule formation, in the areas where they are expressed. We conclude that both genes likely play ancestral roles in organising distal butterfly wing patterns, across pierid and nymphalid butterflies, but are unlikely to be differentiating signalling centres in pierids black spots. The genetic and developmental mechanisms that set up the location of spots and eyespots are likely distinct in each lineage.
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Affiliation(s)
- Jocelyn Liang Qi Wee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S2 01-03, Singapore, 117558, Singapore.
| | - Tirtha Das Banerjee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S2 01-03, Singapore, 117558, Singapore
| | - Anupama Prakash
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S2 01-03, Singapore, 117558, Singapore
| | - Kwi Shan Seah
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S2 01-03, Singapore, 117558, Singapore
| | - Antonia Monteiro
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S2 01-03, Singapore, 117558, Singapore. .,Yale-NUS College, College Ave West, Singapore, 138527, Singapore.
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33
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Brien MN, Enciso-Romero J, Lloyd VJ, Curran EV, Parnell AJ, Morochz C, Salazar PA, Rastas P, Zinn T, Nadeau NJ. The genetic basis of structural colour variation in mimetic
Heliconius
butterflies. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200505. [PMID: 35634924 PMCID: PMC9149798 DOI: 10.1098/rstb.2020.0505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural colours, produced by the reflection of light from ultrastructures, have evolved multiple times in butterflies. Unlike pigmentary colours and patterns, little is known about the genetic basis of these colours. Reflective structures on wing-scale ridges are responsible for iridescent structural colour in many butterflies, including the Müllerian mimics Heliconius erato and Heliconius melpomene. Here, we quantify aspects of scale ultrastructure variation and colour in crosses between iridescent and non-iridescent subspecies of both of these species and perform quantitative trait locus (QTL) mapping. We show that iridescent structural colour has a complex genetic basis in both species, with offspring from crosses having a wide variation in blue colour (both hue and brightness) and scale structure measurements. We detect two different genomic regions in each species that explain modest amounts of this variation, with a sex-linked QTL in H. erato but not H. melpomene. We also find differences between species in the relationships between structure and colour, overall suggesting that these species have followed different evolutionary trajectories in their evolution of structural colour. We then identify genes within the QTL intervals that are differentially expressed between subspecies and/or wing regions, revealing likely candidates for genes controlling structural colour formation. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Melanie N. Brien
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Juan Enciso-Romero
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Victoria J. Lloyd
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Emma V. Curran
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Andrew J. Parnell
- Department of Physics and Astronomy, The University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
| | | | - Patricio A. Salazar
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Pasi Rastas
- Institute of Biotechnology, 00014 University of Helsinki, Finland
| | - Thomas Zinn
- ESRF - The European Synchrotron, 38043 Grenoble Cedex 9, France
| | - Nicola J. Nadeau
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
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34
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McDonald JMC, Reed RD. Patterns of selection across gene regulatory networks. Semin Cell Dev Biol 2022; 145:60-67. [PMID: 35474149 DOI: 10.1016/j.semcdb.2022.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.
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Affiliation(s)
- Jeanne M C McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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35
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Hanly JJ, Livraghi L, Heryanto C, McMillan WO, Jiggins CD, Gilbert LE, Martin A. A large deletion at the cortex locus eliminates butterfly wing patterning. G3 GENES|GENOMES|GENETICS 2022; 12:6517782. [PMID: 35099556 PMCID: PMC8982378 DOI: 10.1093/g3journal/jkac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/21/2022] [Indexed: 11/21/2022]
Abstract
As the genetic basis of natural and domesticated variation has been described in recent years, a number of hotspot genes have been repeatedly identified as the targets of selection, Heliconius butterflies display a spectacular diversity of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here, we sought to identify the mechanism behind an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78-kb deletion at the cortex wing patterning locus, a gene which has been associated with wing pattern evolution in H. melpomene and 10 divergent lepidopteran species. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable while heterozygotes are the targets of artificial selection, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations.
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Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
| | - Luca Livraghi
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christa Heryanto
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Lawrence E Gilbert
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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36
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Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution. Cells 2022; 11:cells11030510. [PMID: 35159319 PMCID: PMC8834487 DOI: 10.3390/cells11030510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 12/18/2022] Open
Abstract
A major driving force behind the evolution of species-specific traits and novel structures is alterations in gene regulatory networks (GRNs). Comprehending evolution therefore requires an understanding of the nature of changes in GRN structure and the responsible mechanisms. Here, we review two insect pigmentation GRNs in order to examine common themes in GRN evolution and to reveal some of the challenges associated with investigating changes in GRNs across different evolutionary distances at the molecular level. The pigmentation GRN in Drosophila melanogaster and other drosophilids is a well-defined network for which studies from closely related species illuminate the different ways co-option of regulators can occur. The pigmentation GRN for butterflies of the Heliconius species group is less fully detailed but it is emerging as a useful model for exploring important questions about redundancy and modularity in cis-regulatory systems. Both GRNs serve to highlight the ways in which redeployment of trans-acting factors can lead to GRN rewiring and network co-option. To gain insight into GRN evolution, we discuss the importance of defining GRN architecture at multiple levels both within and between species and of utilizing a range of complementary approaches.
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37
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Suzuki TK. Phenotypic systems biology for organisms: Concepts, methods and case studies. Biophys Physicobiol 2022; 19:1-17. [PMID: 35749096 PMCID: PMC9159793 DOI: 10.2142/biophysico.bppb-v19.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Design principles of phenotypes in organisms are fundamental issues in physical biology. So far, understanding “systems” of living organisms have been chiefly promoted by understanding the underlying biomolecules such as genes and proteins, and their intra- and inter-relationships and regulations. After a long period of sophistication, biophysics and molecular biology have established a general framework for understanding ‘molecular systems’ in organisms without regard to species, so that the findings of fly studies can be applied to mouse studies. However, little attention has been paid to exploring “phenotypic systems” in organisms, and thus its general framework remains poorly understood. Here I review concepts, methods, and case studies using butterfly and moth wing patterns to explore phenotypes as systems. First, I present a unifying framework for phenotypic traits as systems, termed multi-component systems. Second, I describe how to define components of phenotypic systems, and also show how to quantify interactions among phenotypic parts. Subsequently, I introduce the concept of the macro-evolutionary process, which illustrates how to generate complex traits. In this point, I also introduce mathematical methods, “phylogenetic comparative methods”, which provide stochastic processes along molecular phylogeny as bifurcated paths to quantify trait evolution. Finally, I would like to propose two key concepts, macro-evolutionary pathways and genotype-phenotype loop (GP loop), which must be needed for the next directions. I hope these efforts on phenotypic biology will become one major target in biophysics and create the next generations of textbooks. This review article is an extended version of the Japanese article, Biological Physics in Phenotypic Systems of Living Organisms, published in SEIBUTSU-BUTSURI Vol. 61, p. 31–35 (2021).
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Affiliation(s)
- Takao K. Suzuki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo
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38
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Liao KL, Chang WC, Marcus JM, Wang JN. Mathematical modeling of the eyespots in butterfly wings. J Theor Biol 2021; 531:110898. [PMID: 34508757 DOI: 10.1016/j.jtbi.2021.110898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Butterfly wing color patterns are a representative model system for studying biological pattern formation, due to their two-dimensional simple structural and high inter- and intra-specific variabilities. Moreover, butterfly color patterns have demonstrated roles in mate choice, thermoregulation, and predator avoidance via disruptive coloration, attack deflection, aposematism, mimicry, and masquerade. Because of the importance of color patterns to many aspects of butterfly biology and their apparent tractability for study, color patterns have been the subjects of many attempts to model their development. Early attempts focused on generalized mechanisms of pattern formation such as reaction-diffusion, diffusion gradient, lateral inhibition, and threshold responses, without reference to any specific gene products. As candidate genes with expression patterns that resembled incipient color patterns were identified, genetic regulatory networks were proposed for color pattern formation based on gene functions inferred from other insects with wings, such as Drosophila. Particularly detailed networks incorporating the gene products, Distal-less (Dll), Engrailed (En), Hedgehog (Hh), Cubitus interruptus (Ci), Transforming growth factor-β (TGF-β), and Wingless (Wg), have been proposed for butterfly border ocelli (eyespots) which helps the investigation of the formation of these patterns. Thus, in this work, we develop a mathematical model including the gene products En, Hh, Ci, TGF-β, and Wg to mimic and investigate the eyespot formation in butterflies. Our simulations show that the level of En has peaks in the inner and outer rings and the level of Ci has peaks in the inner and middle rings. The interactions among these peaks activate cells to produce white, black, and yellow pigments in the inner, middle, and outer rings, respectively, which captures the eyespot pattern of wild type Bicyclus anynana butterflies. Additionally, our simulations suggest that lack of En generates a single black spot and lack of Hh or Ci generates a single white spot, and a deficiency of TGF-β or Wg will cause the loss of the outer yellow ring. These deficient patterns are similar to those observed in the eyespots of Vanessa atalanta, Vanessa altissima, and Chlosyne nycteis. Thus, our model also provides a hypothesis to explain the mechanism of generating the deficient patterns in these species.
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Affiliation(s)
- Kang-Ling Liao
- Department of Mathematics, University of Manitoba, Manitoba R3T 2N2, Canada; Department of Biological Sciences, University of Manitoba, Manitoba R3T 2N2, Canada.
| | - Wei-Chen Chang
- Department of Mathematics, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Jeffrey M Marcus
- Department of Biological Sciences, University of Manitoba, Manitoba R3T 2N2, Canada
| | - Jenn-Nan Wang
- Institute of Applied Mathematical Sciences, National Taiwan University, Taipei 10617, Taiwan, ROC
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39
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In vivo visualization of butterfly scale cell morphogenesis in Vanessa cardui. Proc Natl Acad Sci U S A 2021; 118:2112009118. [PMID: 34845021 PMCID: PMC8670486 DOI: 10.1073/pnas.2112009118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Many organisms exhibit functional micro- and nanoscale materials with structural definition and performance that challenge synthetic fabrication techniques, yet we know little about the processes that enable their formation. Using butterfly scales as a model system for functional biomaterials, we establish a timeline of scale formation and quantify relevant structural parameters for developing painted lady butterflies. We overcome challenges of previous efforts by imaging structure formation directly in living organisms, which allows us to continuously observe the evolving wing tissue and the fine details of individual scale cells. Visualization of scale structure formation in live butterflies forms the basis for modeling the underlying biomechanical processes and opens avenues for their translation into advanced fabrication strategies. During metamorphosis, the wings of a butterfly sprout hundreds of thousands of scales with intricate microstructures and nano-structures that determine the wings’ optical appearance, wetting characteristics, thermodynamic properties, and aerodynamic behavior. Although the functional characteristics of scales are well known and prove desirable in various applications, the dynamic processes and temporal coordination required to sculpt the scales’ many structural features remain poorly understood. Current knowledge of scale growth is primarily gained from ex vivo studies of fixed scale cells at discrete time points; to fully understand scale formation, it is critical to characterize the time-dependent morphological changes throughout their development. Here, we report the continuous, in vivo, label-free imaging of growing scale cells of Vanessa cardui using speckle-correlation reflection phase microscopy. By capturing time-resolved volumetric tissue data together with nanoscale surface height information, we establish a morphological timeline of wing scale formation and gain quantitative insights into the underlying processes involved in scale cell patterning and growth. We identify early differences in the patterning of cover and ground scales on the young wing and quantify geometrical parameters of growing scale features, which suggest that surface growth is critical to structure formation. Our quantitative, time-resolved in vivo imaging of butterfly scale development provides the foundation for decoding the processes and biomechanical principles involved in the formation of functional structures in biological materials.
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40
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Lohse K, Wright C, Talavera G, García-Berro A. The genome sequence of the painted lady, Vanessa cardui Linnaeus 1758. Wellcome Open Res 2021; 6:324. [PMID: 37008186 PMCID: PMC10061037 DOI: 10.12688/wellcomeopenres.17358.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual female Vanessa cardui (the painted lady; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 425 megabases in span. The majority of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,821 protein coding genes.
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Affiliation(s)
- Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edingburgh, UK
| | | | - Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Aurora García-Berro
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Darwin Tree of Life Barcoding collective
- Institute of Evolutionary Biology, University of Edinburgh, Edingburgh, UK
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Wellcome Sanger Institute Tree of Life programme
- Institute of Evolutionary Biology, University of Edinburgh, Edingburgh, UK
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Tree of Life Core Informatics collective
- Institute of Evolutionary Biology, University of Edinburgh, Edingburgh, UK
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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41
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Price-Waldman R, Stoddard MC. Avian Coloration Genetics: Recent Advances and Emerging Questions. J Hered 2021; 112:395-416. [PMID: 34002228 DOI: 10.1093/jhered/esab015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
The colorful phenotypes of birds have long provided rich source material for evolutionary biologists. Avian plumage, beaks, skin, and eggs-which exhibit a stunning range of cryptic and conspicuous forms-inspired early work on adaptive coloration. More recently, avian color has fueled discoveries on the physiological, developmental, and-increasingly-genetic mechanisms responsible for phenotypic variation. The relative ease with which avian color traits can be quantified has made birds an attractive system for uncovering links between phenotype and genotype. Accordingly, the field of avian coloration genetics is burgeoning. In this review, we highlight recent advances and emerging questions associated with the genetic underpinnings of bird color. We start by describing breakthroughs related to 2 pigment classes: carotenoids that produce red, yellow, and orange in most birds and psittacofulvins that produce similar colors in parrots. We then discuss structural colors, which are produced by the interaction of light with nanoscale materials and greatly extend the plumage palette. Structural color genetics remain understudied-but this paradigm is changing. We next explore how colors that arise from interactions among pigmentary and structural mechanisms may be controlled by genes that are co-expressed or co-regulated. We also identify opportunities to investigate genes mediating within-feather micropatterning and the coloration of bare parts and eggs. We conclude by spotlighting 2 research areas-mechanistic links between color vision and color production, and speciation-that have been invigorated by genetic insights, a trend likely to continue as new genomic approaches are applied to non-model species.
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42
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Livraghi L, Hanly JJ, Van Bellghem SM, Montejo-Kovacevich G, van der Heijden ESM, Loh LS, Ren A, Warren IA, Lewis JJ, Concha C, Hebberecht L, Wright CJ, Walker JM, Foley J, Goldberg ZH, Arenas-Castro H, Salazar C, Perry MW, Papa R, Martin A, McMillan WO, Jiggins CD. Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius. eLife 2021; 10:e68549. [PMID: 34280087 PMCID: PMC8289415 DOI: 10.7554/elife.68549] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
In Heliconius butterflies, wing colour pattern diversity and scale types are controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knockouts in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.
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Affiliation(s)
- Luca Livraghi
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Joseph J Hanly
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Steven M Van Bellghem
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | | | - Eva SM van der Heijden
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Ling Sheng Loh
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Anna Ren
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | | | - Laura Hebberecht
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Charlotte J Wright
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - Jonah M Walker
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | | | - Zachary H Goldberg
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | | | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del RosarioBogotáColombia
| | - Michael W Perry
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | - Riccardo Papa
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | - Arnaud Martin
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
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43
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Zhang L, Steward RA, Wheat CW, Reed RD. High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui. Genome Biol Evol 2021; 13:evab145. [PMID: 34282459 PMCID: PMC8290113 DOI: 10.1093/gbe/evab145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The painted lady butterfly, Vanessa cardui, has the longest migration routes, the widest hostplant diversity, and one of the most complex wing patterns of any insect. Due to minimal culturing requirements, easily characterized wing pattern elements, and technical feasibility of CRISPR/Cas9 genome editing, V. cardui is emerging as a functional genomics model for diverse research programs. Here, we report a high-quality, annotated genome assembly of the V. cardui genome, generated using 84× coverage of PacBio long-read data, which we assembled into 205 contigs with a total length of 425.4 Mb (N50 = 10.3 Mb). The genome was very complete (single-copy complete Benchmarking Universal Single-Copy Orthologs [BUSCO] 97%), with contigs assembled into presumptive chromosomes using synteny analyses. Our annotation used embryonic, larval, and pupal transcriptomes, and 20 transcriptomes across five different wing developmental stages. Gene annotations showed a high level of accuracy and completeness, with 14,437 predicted protein-coding genes. This annotated genome assembly constitutes an important resource for diverse functional genomic studies ranging from the developmental genetic basis of butterfly color pattern, to coevolution with diverse hostplants.
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Affiliation(s)
- Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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Hanly JJ, Robertson ECN, Corning OBWH, Martin A. Porcupine/Wntless-dependent trafficking of the conserved WntA ligand in butterflies. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:470-481. [PMID: 34010515 DOI: 10.1002/jez.b.23046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 11/11/2022]
Abstract
Wnt ligands are key signaling molecules in animals, but little is known about the evolutionary dynamics and mode of action of the WntA orthologs, which are not present in the vertebrates or in Drosophila. Here we show that the WntA subfamily evolved at the base of the Bilateria + Cnidaria clade, and conserved the thumb region and Ser209 acylation site present in most other Wnts, suggesting WntA requires the core Wnt secretory pathway. WntA proteins are distinguishable from other Wnts by a synapomorphic Iso/Val/Ala216 amino-acid residue that replaces the otherwise ubiquitous Thr216 position. WntA embryonic expression is conserved between beetles and butterflies, suggesting functionality, but the WntA gene was lost three times within arthropods, in podoplean copepods, in the cyclorrhaphan fly radiation, and in ensiferan crickets and katydids. Finally, CRISPR mosaic knockouts (KOs) of porcupine and wntless phenocopied the pattern-specific effects of WntA KOs in the wings of Vanessa cardui butterflies. These results highlight the molecular conservation of the WntA protein across invertebrates, and imply it functions as a typical Wnt ligand that is acylated and secreted through the Porcupine/Wntless secretory pathway.
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Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Erica C N Robertson
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Olaf B W H Corning
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
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45
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The color pattern inducing gene wingless is expressed in specific cell types of campaniform sensilla of a polka-dotted fruit fly, Drosophila guttifera. Dev Genes Evol 2021; 231:85-93. [PMID: 33774724 DOI: 10.1007/s00427-021-00674-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022]
Abstract
A polka-dotted fruit fly, Drosophila guttifera, has a unique pigmentation pattern on its wings and is used as a model for evo-devo studies exploring the mechanism of evolutionary gain of novel traits. In this species, a morphogen-encoding gene, wingless, is expressed in species-specific positions and induces a unique pigmentation pattern. To produce some of the pigmentation spots on wing veins, wingless is thought to be expressed in developing campaniform sensillum cells, but it was unknown which of the four cell types there express(es) wingless. Here we show that two of the cell types, dome cells and socket cells, express wingless, as indicated by in situ hybridization together with immunohistochemistry. This is a unique case in which non-neuronal SOP (sensory organ precursor) progeny cells produce Wingless as an inducer of pigmentation pattern formation. Our finding opens a path to clarifying the mechanism of evolutionary gain of a unique wingless expression pattern by analyzing gene regulation in dome cells and socket cells.
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46
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Van Belleghem SM, Lewis JJ, Rivera ES, Papa R. Heliconius butterflies: a window into the evolution and development of diversity. Curr Opin Genet Dev 2021; 69:72-81. [PMID: 33714874 DOI: 10.1016/j.gde.2021.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 10/21/2022]
Abstract
Butterflies have become prominent models for studying the evolution and development of phenotypic variation. In Heliconius, extraordinary within species divergence and between species convergence in wing color patterns has driven decades of comparative genetic studies. However, connecting genetic patterns of diversification to the molecular mechanisms of adaptation has remained elusive. Recent studies are bridging this gap between genome and function and have driven substantial advances in deciphering the genetic architecture of diversification in Heliconius. While only a handful of large-effect genes were initially identified in the diversification of Heliconius color patterns, recent experiments have begun to unravel the underlying gene regulatory networks and how these have evolved. These results reveal an evolutionary story of many interacting loci and partly independent genetic architectures that underlie convergent evolution.
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Affiliation(s)
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA; Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edgardo S Rivera
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; Chairs of Biomaterials, University of Bayreuth, Bayreuth, Bayern, Germany
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico.
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47
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Saranathan V, Finet C. Cellular and developmental basis of avian structural coloration. Curr Opin Genet Dev 2021; 69:56-64. [PMID: 33684846 DOI: 10.1016/j.gde.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Vivid structural colors in birds are a conspicuous and vital part of their phenotype. They are produced by a rich diversity of integumentary photonic nanostructures in skin and feathers. Unlike pigmentary coloration, whose genetic basis is being elucidated, little is known regarding the pathways underpinning organismal structural coloration. Here, we review available data on the development of avian structural colors. In particular, feather photonic nanostructures are understood to be intracellularly self-assembled by physicochemical forces typically seen in soft colloidal systems. We identify promising avenues for future research that can address current knowledge gaps, which are also highly relevant for the sustainable engineering of advanced bioinspired and biomimetic materials.
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Affiliation(s)
- Vinodkumar Saranathan
- Division of Science, Yale-NUS College, 10 College Avenue West, 138609, Singapore; NUS Nanotechnology and Nanoscience Initiative, National University of Singapore, 117581, Singapore.
| | - Cédric Finet
- Division of Science, Yale-NUS College, 10 College Avenue West, 138609, Singapore
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48
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Does Structural Color Exist in True Fungi? J Fungi (Basel) 2021; 7:jof7020141. [PMID: 33669274 PMCID: PMC7920071 DOI: 10.3390/jof7020141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/25/2022] Open
Abstract
Structural color occurs by the interaction of light with regular structures and so generates colors by completely different optical mechanisms to dyes and pigments. Structural color is found throughout the tree of life but has not, to date, been reported in the fungi. Here we give an overview of structural color across the tree of life and provide a brief guide aimed at stimulating the search for this phenomenon in fungi.
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49
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The evolution of structural colour in butterflies. Curr Opin Genet Dev 2021; 69:28-34. [PMID: 33540167 DOI: 10.1016/j.gde.2021.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/21/2020] [Accepted: 01/01/2021] [Indexed: 01/23/2023]
Abstract
Butterflies display some of the most striking examples of structural colour in nature. These colours originate from cuticular scales that cover the wing surface, which have evolved a diverse suite of optical nanostructures capable of manipulating light. In this review we explore recent advances in the evolution of structural colour in butterflies. We discuss new insights into the underlying genetics and development of the structural colours in various nanostructure types. Improvements in -omic and imaging technologies have been paramount to these new advances and have permitted an increased appreciation of their development and evolution.
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50
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Aguillon SM, Walsh J, Lovette IJ. Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype. Proc Biol Sci 2021; 288:20201805. [PMID: 33468000 DOI: 10.1098/rspb.2020.1805] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers-yellow-shafted and red-shafted flickers-to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across approximately 7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wing and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.
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Affiliation(s)
- Stepfanie M Aguillon
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Jennifer Walsh
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
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